Browsing by Author "Wu, Le-Shin"
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Item ACI-REF Mission: User Sensitivity 101(2015-09-02) Ganote, Carrie; Wu, Le-Shin; Doak, ThomasItem Automating work in Galaxy(2015-08-12) Ganote, Carrie; Wu, Le-Shin; Doak, ThomasItem Computing challenges in working with genomics-scale data(2014-07-23) Wu, Le-Shin; Ganote, CarrieIntroduction to the computing challenges in working with genomics-scale data and the possible solutions.Item Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome(ACM, New York, NY, 2015-07-26) Wu, Le-Shin; Ganote, Carrie; Doak, Thomas; Barnett, William K.; Mockaitis, Keithanne; Stewart, Craig A.Today's genomics technologies generate more sequence data than ever before possible, and at substantially lower costs, serving researchers across biological disciplines in transformative ways. Building transcriptome assemblies from RNA sequencing reads is one application of next-generation sequencing (NGS) that has held a central role in biological discovery in both model and non- model organisms, with and without whole genome sequence references. A major limitation in effective building of transcriptome references is no longer the sequencing data generation itself, but the computing infrastructure and expertise needed to assemble, analyze and manage the data. Here we describe a currently available resource dedicated to achieving such goals, and its use for extensive RNA assembly of up to 1.3 billion reads representing the massive transcriptome of loblolly pine, using four major assembly software installations. The Mason cluster, an XSEDE second tier resource at Indiana University, provides the necessary fast CPU cycles, large memory, and high I/O throughput for conducting large-scale genomics research. The National Center for Genome Analysis Support, or NCGAS, provides technical support in using HPC systems, bioinformatic support for determining the appropriate method to analyze a given dataset, and practical assistance in running computations. We demonstrate that a sufficient supercomputing resource and good workflow design are elements that are essential to large eukaryotic genomics and transcriptomics projects such as the complex transcriptome of loblolly pine, gene expression data that inform annotation and functional interpretation of the largest genome sequence reference to date.Item Galaxy for Data Provenance(2014-07-16) Ganote, Carrie; Wu, Le-Shin; Doak, ThomasItem Introduction to Galaxy 2015(2015-08-12) Ganote, Carrie; Wu, Le-Shin; Doak, ThomasItem Introduction to genomics software use on high performance computing systems(2014-07-22) Wu, Le-Shin; Ganote, Carrieintroduction to running genomics softwares on a high performance computing systems.Item Moving Large Data to Galaxy(2014-07-16) Ganote, Carrie; Wu, Le-Shin; Doak, ThomasItem The National Center for Genome Analysis Support(2014-11-16) Ganote, Carrie; Wu, Le-Shin; Doak, Thomas; Barnett, WilliamItem National Center for Genome Analysis Support (Poster)(2012) Doak, Thomas G.; Wu, Le-Shin; Stewart, Craig A.; Henschel, Robert; Barnett, William K.Item The National Center for Genome Analysis Support (Poster)(2012-09) Doak, Thomas G.; LeDuc, Richard; Wu, Le-Shin; Stewart, Craig A.; Henschel, Robert; Barnett, William K.Item National Center for Genome Analysis Support Leverages XSEDE to Support Life Science Research(ACM, 2013-07-23) LeDuc, Richard D.; Wu, Le-Shin; Ganote, Carrie L.; Doak, Thomas; Blood, Philip D.; Vaughn, MatthewItem The National Center for Genomic Analysis Support: creating a national cyberinfrastructure environment for genomics researchers.(2015-05-16) Barnett, William; Doak, Thomas; Wu, Le-Shin; Ganote, CarrieItem Quality Control and Assessment of RNA-Seq Data(2014-07-22) Ganote, Carrie; Podicheti, Ram; Wu, Le-Shin; Doak, ThomasItem Results of the 2014 Survey of NSF-funded researchers on their bioinformatics (genomics) needs(2014-12-31) Doak, Thomas G.; Barnett, William; Ganote, Carrie; Wu, Le-ShinItem RNA-Seq Demo on Galaxy(2015-08-12) Ganote, Carrie; Wu, Le-Shin; Doak, ThomasItem RNA-Seq Demo on Galaxy(2014-07-16) Ganote, Carrie; Wu, Le-Shin; Doak, ThomasItem Solving the challenges of complex genome analysis collaborations on-line using XSEDE resources (Poster)(Plant and Animal Genomics 2018, 2018-01-15) Ganote, Carrie; Sanders, Sheri; Wu, Le-Shin; Doak, Tom; Mockaitis, KeithanneWhole genome reference and functional genomics projects most often benefit from a diversity of expertise and the integrated contributions of multiple research groups. The importance of web-enabled data sharing and open access software to progress in genome research is indisputable. Dissemination of genome resource information through internet-based resources, especially customizing and encouraging the optimal use of analysis tools to serve a specific research community, often lags behind data generation. This lag can inhibit biological interpretations and downstream experimentation, much of which should be undertaken before a genome resource project is completed. File systems for storing data and analysis outputs of today’s project standards must be large and secure, and must offer sustained access to fulfill the hosting requirements an active and dispersed research community needs. Users must interact with a computing resource powerful enough to get their jobs done, and sites must be expandable and flexible to accommodate a growing demand for intra-genera comparisons and pan-genomics of a species. We have been using NSF XSEDE computational resources including Jetstream along with the High Performance Computing systems of Indiana University to meet these challenges for a variety of collaborative plant genomics studies. Currently these efforts are impacting metabolic gene discovery in the tetraploid Arachis hypogaea and whole genomic reference studies of the tetraploid Coffea arabica and its diploid progenitors. Here we show practical examples of XSEDE resource use and development that may benefit other genomic research groups seeking to increase the effectiveness of their computing and collaboration.Item Using Prior Knowledge to Improve Scoring in High-Throughput Top-Down Proteomics Experiments(2013-06-08) LeDuc, Richard D.; Wu, Le-Shin